Equestria and the Time Lord Episode 4: Shadow Over the Sun
by The Orwellian Writer
Summary: The Doctor has come to watch Equestria's first eclipse in recorded history. But the eclipse gives way to panic through the populace. This panic has unleashed an evil that nopony anywhere has been free from for 66 years. This evil has emerged from the shattered soul of Princess Luna, and it may be the Doctor's skepticism of raising the Sun and Moon that will save them all.
1. Prologue: Four Hundred Dawns

Equestria and the Time Lord Episode 4: Shadow Over the Sun

Prologue: Four Hundred Dawns

**=Gaia, Equestria, Canterlot, Canterlot Royal Palace, 1066 C.E. =**

It was sometime in the middle of the night. The Moon was right there in the middle of the sky. Princess Luna was looking at it with a somber look. She sighed and walked back into the room. She stretched and lay down in her bed. She had no need for sleep, but she could still think of reasons she needed to relax, but she had many things holding her back from total relaxation. Her royal duties, all that she must tend to, and most of all the ever present shadow off…

'_The nightmare of Nightmare Moon?' _Said a dark version of her own voice inside her head.

'What?' Luna thought in her head in fear.

'_Nightmare Moon, the embodiment of all your jealousy and anger? The thing living in your shadow and legacy that you can't bear to think about but slithers into your mind every day in your every moment of the 66 years you have deluded yourself into thinking you were truly free?' _the voice continued.

'I am free.' Luna thought indignantly.

'_There is still fear. There is still hate. There is still a lost glimmer of me living in your mind, and you may spend your day running and running from the fear, the hate, but you can't move anywhere farther from your own shadow.' _The voice argued.

'I will not give into you. I am no longer Nightmare Moon! I AM NOT YOU!' Luna screamed in her head.

'_Tomorrow the sun will rise, but then it will give away to shadow. There will be eternal night by your power. And when all who you care about, all that you know, all that you will come to believe in cannot stop it, when you see what __**magic**__ is really worth, you will be broken and nothing can stop me from coming forward and the both of us will be reunited.' _the voice toldevilly.

'What are you talking about? How can you make eternal night from daytime? That is impossible!' Luna thought angrily.

'_Tomorrow is the day of Darkness. Tomorrow is the first eclipse.' _The voice said as it began to reach a hoof through her shadow.

'What is an eclipse?' Luna asked as the hoof grabbed her and she lost consciousness.

**=Gaia, Equestria, Canterlot, Canterlot City Streets, 1066 C.E. =**

The Doctor looked up from the console as the TARDIS materialized. "This is very exiting!" he said as he ran over to a TARDIS closet and few it open, dodging a large pile of stuff coming out.

"Where and when are we?" Daring Do asked.

"We're in the city of Canterlot in the year 1066." Romana read off from the scanner.

"Canterlot! How wonderful! Canterlot is a very great city! I've been there several times myself." Daring Do said.

"Exactly!" The Doctor said as he pulled out a large telescope and ran out of the TARDIS holding it.

Daring Do and Romana followed him out to see the Doctor positioning the telescope in the direction of the sunlight, which was now making its first traces over a hill.

Daring Do walked over to him. "It's a pretty sunrise, but I doubt it's why we came here."

"Have you ever had an eclipse before?" The Doctor said.

"What's an eclipse?" Daring Do asked.

"An eclipse." K9 said next to her, causing her to jump. "An eclipse is an astronomical event when an astronomical object is temporarily obscured, either by passing into the shadow of another body or by having another pass between it and the viewer. A solar eclipse is when the Moon passes in between the planet and the Sun. A lunar eclipse is when the planet is positioned directly in between the Sun and the Moon, causing it to turn a red color. Early primitive cultures believed that eclipses were a sign that they had angered their gods and panicked at them." He described.

"And in precisely 5 hours 47 minutes, we are looking at a total solar eclipse!" The Doctor said excitedly.

"How is this of major significance?" Daring Do asked.

"In 1919 on the planet Earth, a scientist named Albert Einstein photographed an eclipse and used it to prove the theory of relativity. He became known as one of the greatest scientists of all time! And I believe them because I met him at least a hundred times! Before that, in 1868, an eclipse was used to discover the chemical properties of the Earth's Sun! An eclipse in 1842 identified the corona as part of the Sun's atmosphere. So many astronomical discoveries were made because of eclipses and you bet that I'm going to be here to witness the first eclipse in recorded history, because who knows what is going come from it! And frankly, how can you have never had an eclipse before, they are a regularly scheduled astronomical event that cannot be held off!"

I guess Princess Celestia and Princess Luna never scheduled one before." Daring Do said.

"What on Earth are you talking about?" The Doctor asked as he continued to follow the Sun with his telescope.

"You see Doctor, every morning; Princess Celestia raises the Sun with magic, and then lowers the Sun at night. Every night Princess Luna raises the moon, and then lowers the moon in the morning. I can't think that they would have a reason to put an eclipse in there." Daring Do explained.

The Doctor stared blankly at her for at least two minutes. Then, he snorted. This snort quickly escalated into…"Ha ha ha Ha Ha Ha Ha Ha HA HA HA HA HA HA HA HA HA!"

Daring Do glared at him as The Doctor fell to the floor laughing like a total maniac. She heard him all too well. Unfortunately, those that weren't woken up by The Doctor's rambling session about eclipses were certainly woken up by him laughing.

The Doctor stood up as his laughter died down. "You may not have been able to tell, but I don't believe in magic."

Daring Do wanted to answer, but was poked in the back by a spear that was held by a Royal Guard, who looked rather tired. "You're disrupting the peace. You will come with me." The Guard said.

"With pleasure. I'd rather like to have a word with this Princess Celestia and discuss with her a few words about the scientific fundamentals of how it isn't possible to raise the Sun or the Moon, and make her understand the prospect of orbit. Come to think of it, if they still think the planet is flat, I am getting out of here and taking off 200 years in the future or so…" The Doctor began as Daring Do rammed her hoof into his side to stop his rambling before the Guard did so in a more aggressive fashion. They all began to walk away.

Miles away, they were being watched from a balcony. On this balcony was Princess Luna. But it wasn't Princess Luna. Princess Luna was unconscious in her bed, and her shadow was stretching out to a transparent copy of Princess Luna with catlike eyes. "5 hours and 30 minutes to the first eclipse. No one will know what has caused it. The panic will bring death to them all. The ones you will come to trust are here. There is so much you will never know. Your mind is full of distorted holes. It will not take much to make it shatter." The shadow receded into Luna's body, which began to shiver and convulse.


	2. Chapter 1: Coronas of the Sun

Chapter 1: Coronas of the Sun

**=Gaia, Equestria, Canterlot, Canterlot Royal Palace Grounds, 1066 C.E. =**

The Doctor moved along, goaded by the push of a long spear from behind him. "Keep moving," the Royal Guard said to him. "You will be taken directly to the Royal Court."

"Well how delightful." The Doctor said over cheerfully.

The Guard rolled his eyes in annoyance, and pushed them into the halls of the castle.

"You know, I find the legal system of this Royal Court to be obscenely uptight." Romana noted. "We didn't do anything that terrible."

"Says the girl who appears to be good friends with the obscenely dressed stallion who talks obscenely too much." The Guard said sarcastically.

"I agree with him on that last part. You talk too much." Daring Do said.

"I know I talk too much. That's why I keep talking." The Doctor said.

The Guard pushed them through a very tall golden colored door, and walked away, rather happy not to have to listen to them anymore.

The Doctor, Romana, and Daring Do began walking through the rather lengthy room, admiring the many decorated glass windows that the Doctor figured depicted multiple notable historic events. In fact, most of them were used as an illustration in the detailed book he read about Equestrian history. He admired the fact that many more would come to be made in the future. Heck, they would even make one about the eclipse he had come to watch. He could tell this would be exciting to watch.

At the end of the room were five thrones for all of the Canterlot royalty. They were certainly a colorful bunch, all right. In the middle, there was a white alicorn (had both a horn and wings) with a flowing green, blue, and pink mane, with a one of those sun markings on her flank. The Doctor could tell she was the big leader. On the left side of her was a purple alicorn with a purple mane with a pink stripe in it, who also had a pink star marking with white stars around it. Next to her was a white unicorn with a blue mane and a shield with a star over it marking. On the end of the right side was a pink alicorn with a pink, purple, and yellow mane, and had the marking of a teal heart. Deductive reasoning told the Doctor that these last two were rulers of another land, but happened to be in town as of now. He did notice that the throne right next to the one with the sun mark, that he guessed was Princess Celestia, was empty, but it was decorated for who he guessed was Princess Luna.

He stepped forward. "Hello." He said simply.

"Hello sir." Princess Celestia said. "Now I have a question for you. Why were you waking all those ponies up at 4 in the morning?"

"Before I answer that, let me tell you our names." The Doctor said. "I'm the Doctor, this is Romana, and this is Daring Do."

"That is nice, but you still haven't answered the question." The purple one snapped.

"Princess Twilight, please. They were pushed in here quite fast, and we didn't even ask their names." Princess Celestia turned to the Doctor. "I suppose we will need no introduction."

"Actually, I don't know any of you at all." The Doctor half-lied.

Princess Celestia actually seemed a little taken aback by this. "Well, I am Princess Celestia, the ruler of Equestria. My sister, Princess Luna, is currently asleep right now. She is very stressed out. This was my former student, Twilight Sparkle, who, 63 years ago, turned into an alicorn princess. This is her brother, Shining Armor, who became royalty and the ruler of the Crystal Empire after he married her, Princess Cadance."

"Nice to meet you all. Now to answer your question, I was just making an early set up for the eclipse at 10:47."The Doctor said.

"What in Equestria is an eclipse?" Princess Twilight asked.

"I swear, why must everypony ask that? Don't you think it's great that I remember that it's everypony instead of everybody? I was only told once, and now I've always figured out to say that every time." The Doctor said, getting off topic.

"Are you even listening to us? What is an eclipse?" Princess Twilight asked.

"Oh, an eclipse is just when the moon passes between the Sun, obscuring it from view. I came here to get a good view of it. Sorry about waking a few thousand ponies up. It's just very exciting." The Doctor said.

Princess Celestia chuckled. "That cannot happen. My sister would not drive the Moon over the Sun."

The Doctor outright laughed. "Nopony can move the Sun. How can you move something so far away? How can you move something so big? Besides, how can you move something when magic doesn't exist?"

All the members of the Royal Court burst out laughing. "If there is no such thing as magic, what is this then?" Princess Celestia said as she lifted him up with her supposed magic.

"Biologically produced telekinetic energies, but that's it." The Doctor said as he was lowered onto the ground, crossing his hooves unhappily

"If you are insane enough to not believe in magic, you are fighting a losing battle trying to convince us of such." Princess Celestia said, still chuckling.

The Doctor began to storm out of the room. "Magic, eh? Magic? If you want magic, I'll show you something incredible, and there is no magic involved. See you in approximately 5 hours and 40 minutes to the second, or at least from your point of view!" And then he was gone.

"Where is he going?" Princess Celestia asked.

"5 hours and 40 minutes from now, about." Romana said.

5 hours and 39 minutes later, much had happened. Society in the city had gotten started, and the Royal Court had gotten started with their full Royal duties. Romana and Daring Do were still in the room, who were entertaining themselves by reading the story behind each of the glass windows, with Daring Do being more interested in the ones from the future. They had pretty much settled down, when all of a sudden…

The TARDIS rematerialized in the middle of the room, with the Doctor stepping out. "5 hours and 40 minutes on the dot, and no magic involved." he said.

The Royal Court clapped. "Nice magic." Princess Twilight said. "What is the trick?"

"But-"The Doctor said. "THERE IS NO SUCH THING AS MAGIC! No come with me!" he began walking away. The Royal Court sighed and got up and followed him.

"Has it even surprised you or worried you that Princess Luna is still not here?" The Doctor asked.

"Luna?" Princess Celestia said. "I suppose it should, but I guess if just didn't…"

"That's a powerful psychic blocking right there." The Doctor said as he walked into Princess Luna's room.

As soon as he was in the room, he walked over and stepped onto the balcony. "The eclipse should be in only two minutes."

"There can be no such thing as an eclipse!" Princess Celestia said as she walked over to Princess Luna and inspected her.

"She's still alive, so you can come over." The Doctor said.

With some hesitation, Princess Celestia, the rest of the Royal Court, and Romana and Daring Do walked over to the balcony

As they watched in shock, the Sun became passed over by a darkened extraterrestrial body, completely covering it, with only a ring of light around it shining over, darkening everything.

"That's impossible…" Princess Celestia said in shock.

Suddenly, there was a blood-curdling screech of death from behind them.


	3. Chapter 2: The Day of Darkness

Chapter 2: The Day of Darkness

**=Gaia, Equestria, Canterlot, Canterlot Royal Palace, 1066 C.E. =**

The Doctor whirled around to see the source of the scream. When he saw it was Princess Luna, he motioned for his companions to come over to examine her. He saw, however, that only Romana had come over. "Where are the rest of those busybodies?" he asked himself. He turned over to see where the Royal Court and Daring Do were at. He groaned when he saw that they were still standing, watching the eclipse, mesmerized. "That's not good for your eyes, you know." He said.

They still didn't budge. He looked over the balcony to see into the city streets. Everypony he could see was also watching the eclipse, mesmerized. He pulled a little metal ring out of his pocket and aligned it directly with the eclipse. The ring began to glow a purple pink color that resonated through the room; he waved it through the room to every pony in the room with a horn. "Somepony here is reflecting a psychic mesmerism signal off the Moon telepathically, and not by magic." The Doctor said.

"Doctor, I don't believe in magic either, but there's simply no point in trying to change their entire culture." Romana told him.

"That is good advice Romana." The Doctor said. "Which I choose to completely ignore." The metal ring began to glow a blue color, and The Doctor walked over to Princess Luna. "Here is the source." He said as he waved it over her body. He slipped it over her glowing horn, which stopped glowing. Immediately, panicked screams erupted from behind them.

"Do you think they were mesmerized long enough to establish a psychic breakdown?" Romana asked as she examined the ring.

"I don't know. It could well be. It has certainly had enough time to use Princess Luna as a conduit." The Doctor deduced. "Unless it was already there in the first place." He walked over to the Royal Court, who were panicking but not screaming, and Daring Do, who only seemed surprised but not entirely panicked. "How are you all doing?"

"This can't be possible." Princess Twilight said. "Princess Celestia, why would you schedule the Sun to be covered up?" She was obviously very loyal to Princess Celestia and completely confused as to why this was happening.

"I…I did not." Princess Celestia said who was equally confused.

"Then why did it happen?" Shining Armor asked impatiently.

"I do not know." Princess Celestia said simply.

"Don't be so afraid, it's only a simple eclipse."The Doctor said, not entirely worried at all.

"We do not know why the eclipse has happened. Our magic cannot bring the Sun back to the light. The ponies are terrified. We are all afraid." Princess Celestia said.

"I can understand that, but what you think is magic cannot move the Moon out of the way of the Sun, only the rotational orbit of the Moon and the Sun will do that." The Doctor said.

"Rotational orbit?" Princess Celestia asked, confused.

Daring Do groaned. She knew very well how this was going to end, and nopony would be any less confused when it was all over.

"Yes, when the planet goes in a rotational pattern around the Sun, which is gigantic, and it seems like night because the planet turns in a direction where the other side of the planet is facing the Sun, with some of the light illuminating the Moon, making it look brighter.

"You cannot be serious. You must be truly mad to give into these idiotic untruths." Princess Celestia said, laughing.

"I am serious. And frankly, is it considered improper to use conjunctions, or have you just forgotten how? And another thing, did anypony ever tell you that the planet was round, and you didn't believe them?" The Doctor said.

"Of course she didn't, because the Planet Gaia is flat." Princess Twilight interjected.

And now it was the Doctor's turn to laugh out loud. "Oh my God, they still do think that the planet is flat! I can't believe it! Ah ha ha! They don't even understand the law of gravity yet!" Then the Doctor stopped laughing. "It appears I will have to take matters into my own hooves."

"Oh no…" Romana said as she rubbed her temples.

Just then, the eclipse began to end. "See, nothing to worry about." The Doctor said happily. "Your eclipse ended, and magic didn't do anything about it."

"No…" Luna muttered weakly as she coughed.

"Luna?" Princess Celestia said as she stepped forward.

"Uh, Doctor?" Romana said as she looked up towards the eclipse.

"Oh my…" The Doctor said in shock.

It wasn't the Moon moving away from the Sun. The light of the Sun was disappearing from behind the Moon, making it become clearer and clearer.

"Okay, that's a little unusual, but I can think of at least a million scientific explanations for this kind of phenomena." The Doctor began before he was stopped by a hoof slapping him.

"WE DO NOT HAVE TIME FOR SCIENTIFIC EXPLANATIONS!" Daring Do yelled, obviously panicked. "THE SUN JUST **DISAPPEARED**, AND WHO KNOWS WHAT WILL HAPPEN NEXT!"

"_What will happen next is the death of everypony in the room, and across this entire planet."_ Said a loud voice coming from Princess Luna's mouth.

"Oh no…" Princess Celestia said as she looked over to the Moon.

The moonlight was beginning to glow very intensely. The light seemed to be focusing into a concentrated beam.

"We may want to get out of here." The Doctor said.

The four awake members of the Royal Court jumped off the balcony and began flying down to the ground. Daring Do followed after them, with Romana riding on her because she couldn't fly. "Doctor, come on!" Romana called out.

"I've got to get back to the TARDIS!" The Doctor called out as he ran out of the room and through the halls towards the Throne room.

The Royal Court, Daring Do, and Romana went onto the ground and landed. They were about to go back in, when suddenly…

The beam of moonlight reached the entire Canterlot Castle, completely covering it as it warped around and completely disappeared. All the nearby guards were shocked and walked over to where it once was.

"Luna was still in there." Celestia said, horrified.

"And so was the Doctor." Romana noted.

And then there was nothing they could do. The moon went completely dark, making everything completely unable to be seen. The Day of Darkness had truly begun.

And then the_ real _panic started.


	4. Chapter 3: The Roof of the World

Chapter 3: The Roof of the World

**=The Moon of the Planet Gaia, 238,857 Miles Above in Orbit, Canterlot Royal Palace, Historical Windows, 1066 C.E. =**

The Doctor panted as he realized what head just happened. He was only about 10 yards away from the TARDIS, when suddenly he felt a heat rush moved across his body. "Okay. Where are we now?" he asked himself. He decided to go back up to Luna's room, as he could tell she was still in the palace. He walked out of the room and began climbing through the halls. He got to the stairs that led up to Luna's room. He walked up them and entered the room. He walked over to the balcony to inspect where he and the entire palace had been transported to. He looked over the balcony, and saw…

Nothing. There was not enough light anywhere for him to see anything. It was just inky, no, pure and total darkness as far as the eye, and probably far beyond that, could see. "Well, this is sort of frightening." The Doctor said to himself.

He then walked over to where Luna was at. He could see that she was now using her horn for something different than the psychic field he had inhibited. Undoubtedly it was what was being used to keep them here, and probably blocking the TARDIS materialization field, and who knows what else. He sighed. "I think I'm going to need a few more rings." He mused to no one in particular.

**=Gaia, Equestria, Canterlot, The Panicked City Streets of Canterlot, 1066 C.E. =**

Considering it was recently made impossible to see anything without something like candle, of which it was almost impossible to find, you can imagine the absolute pandemonium that was running around in the streets. Ponies were running around aimlessly, almost always crashing into things or other ponies. It was still uncertain if there were any fatalities or more likely, major or minor injuries. Other ponies had been too scared to move, so they walked into a corner and allowed their hooves to buckle, and most of them were relatively safe. Panic took the ponies so quick that all the unicorns forgot they could perform an illumination spell. Romana, Daring Do, Princess Celestia, Princess Twilight, Shining Armor, and Princess Cadence had all gotten separated quite a long time ago trying to find their way through the darkness. The Royal Guard that had been nearby wanted to protect them, but had been unable to find them due to how dark it was, so they decided to stay nearby the place where the Royal Palace had once been.

One of these guards didn't notice a shadow approaching him, as it blended in with everything. It suddenly began to enter his body, pressing down his every thought with its own. The Guard fell to the floor. He emerged with catlike irises, although no one can see them in the dark. He could see everything as light as day. He had night vision now. He began walking away, prowling around for one the Royal Court, or the Doctor's friends.

He walked about in the streets, not caring if a random pony ran into him at top speed in a panic. He pushed ponies that were in his way out of his way. He searched through the streets ever vigilantly, not missing one pony in the streets along the way. He suddenly caught sight of Princess Cadence right there in a building a few feet away, trying to avoid the panic that not even she could stop. He walked through the streets towards the building. He knocked on the door. A female mare stuck her head out, apparently not willing to let in the complete chaos out there. Realizing that he wouldn't be able to get in, he touched the mare. The entity in control of his mind left him and travelled through his nerve impulses into the other mare, who shot back, now controlled. The Guard fell down dead, his mind too compressed to regain control.

The mare walked around the makeshift refugee camp over to Princess Cadence, who was sitting in the light of a single candle. She didn't really notice when the mare's face emerged from the darkness and into the light of the candle. The mare reached her hoof forward.

**=The Moon of the Planet Gaia, 238,857 Miles Above in Orbit, Canterlot Royal Palace, Princess Luna's Room, 1066 C.E. =**

The Doctor walked around the balcony in Princess Luna's room, trying to figure out what he would do next. He had no idea where he was, he had already checked that he couldn't use the TARDIS, he couldn't wake up Princess Luna for help, and he was rather frustrated. Then he was struck by an idea.

"I'll check my pockets!" The Doctor realized. He stretched out and opened his pocket. After he pulled out the extensible amount of bags of jelly babies he had in his pocket, he finally managed to pull out something he could actually use. "A torch!" he said as he pulled out a flashlight (of torch as they knew it in Britain.) He turned on the flashlight and began using it to see what was below him. He saw a gray, rocky crater. "So we're on this planet's Moon." He deduced to himself. He moved it over a fluctuating field that stretched thin over the whole palace. "That's an air generating field. If I divert that one task, it will give me about ten minutes or so to get back into the TARDIS and dematerialize it back on the planet. On the down side, I won't have any air to breathe of any sort." He said to himself. He sighed, and smiled. "Well here we go!" He took a deep breath, and jumped off the balcony.

**=Gaia, Equestria, Canterlot, The Panicked Streets of Canterlot, 1066 C.E. =**

Princess Cadence walked through the streets, fully under the influence of the entity that had controlled the Guard and the mare. She now had Princess Celestia in her sights. Princess Celestia was what she really wanted. She would be the bargaining chip that would break Princess Luna's mind and allow her total control.

Princess Celestia had tried her hardest to quell the panic in the streets, but found that it was too absolute. She sighed. If Discord wasn't reformed, he would love this. So far, she was one of the only ones who hadn't forgotten to use an illumination spell.

"Cadence!" she said happily when she saw her coming into her sight. Then she saw the catlike eyes. "Oh no."

Princess Cadence came closer and closer, a crooked smile etched into her face.


	5. Chapter 4: The Nightmare Begins

Chapter 4: The Nightmare Begins

**=The Moon of the Planet Gaia, 238,857 Miles Above in Orbit, Canterlot Royal Palace, Palace Grounds, 1066 C.E. =**

The Doctor felt a sensation of having all the air ripped right out of his lungs as he ripped out of the oxygen field as gravity got weaker around and he floated down to the surface of the Moon. He used his superior respiratory system to hold in air in the middle of the vacuum of space. He ran across the surface as he tried to find his way to the window of the room that the TARDIS was inside. He recognized the decorated window in reverse just a short distance upwards from the ground. He tried to scale the stone walls of the castle, finding it very difficult to do with hooves, and made it up to the outside of the window, and pulled out his sonic screwdriver and held it up to the window, utilizing it to crack open the window and get inside to the room. When he got inside, he noted that all the air had been sucked out of the room when he disrupted the air generating field. His sonic screwdriver, which was still turned on, accidentally cracked all the windows in the room and made them all smash into little shards of glass.

'_Oh well. They can always rebuild them later._' The Doctor thought to himself with the little energy he had.

He ran through the room, trying to make it to the TARDIS before his respiratory system gave out. He made it to the TARDIS, pulled the key out of his pocket, and opened the door.

Of course, there was still no oxygen in the TARDIS. He got up, and shut the doors. The Doctor then pressed a button on the console. He took a deep breath of air as the TARDIS filled with air and he began to dematerialize the TARDIS to a couple locations.

**=Gaia, Equestria, Canterlot, The Panicked Streets of Canterlot, 1066 C.E. =**

Princess Celestia tried to flee through the streets, trying to dodge and avoid the possessed Princess Cadence. She knew that this wasn't very likely to happen, as her pursuer could see perfectly in the dark, and could fly. She mentally slapped her forehead. Why did everypony forget how to fly in tight circumstances? She extended her wings, and took off into the blackened skies of the city. She could feel Princess Cadence flying up right behind her. She couldn't help but wonder pessimistically how everything always, no matter how great and peaceful and prosperous things were at one time, eventually some terrible disaster would come crashing through out of absolutely unexpected and unfathomable places.

Suddenly, her thoughts were both ended and confirmed by Daring Do crashing directly into her through the darkness into her face. Pain rocketed through her body as her nose began to bleed, and she lost feeling in her wings as she fell towards even more pain. Daring Do, even though she was probably even more hurt, caught her and held her up, not paying attention to the fact that she was heavy. She set her down on the ground. She examined her, using what little medical experience she had picked up along the way. Princess Cadence came up behind her and touched her on the back.

The entity moved through Princess Cadence's nerves and travelled into her body. Princess Cadence collapsed unconscious, severely weakened. Daring Do, as she became possessed, grabbed Princess Celestia by the arm. She extended her connection to her body to move her mouth. "You cannot run." She said evilly. "All non alicorn ponies who are possessed by my will die due to the strain of my control. If you attempt to struggle, she will be dead before you can do anything to stop me. Do you understand?"

Princess Celestia nodded weakly. Daring Do grabbed her by the neck and pulled her away.

In another part of the city, Romana was running through the streets, finding her way around with a flashlight she had pulled out of her pocket. She was doing a decent job of survival, but then her flashlight flickered and died. "Terrific." She sighed sarcastically.

Suddenly, there was a flashing light above her, accompanied by the sound she had heard a very many times. She smiled, stepped forward and pushed, walking into the TARDIS and walking up to the Doctor. "Where were you?" she asked him.

"On the moon." The Doctor said bluntly. "Now we need to find the others and get back to said Moon, because Princess Luna is up there, and her body appears to be what turned out the light everywhere."

"Well where are the others?" Romana asked.

"I'm locking on their biological signatures that I just so happened to have scanned when I materialized in the middle of the room they were all sitting in." The Doctor said as he read off on a screen. "Shining Armor appears perfectly fine, not far from us either. Princess Cadence is unconscious, we may want to leave her alone or perhaps not, we don't have much time. Princess Twilight, also fine, in the same place as Shining Armor. Princess Celestia and Daring Do are in the same place but their energy is all funny. Now, let's go!"

He pressed a lever on the TARDIS console, and the TARDIS began to dematerialize and rematerialize somewhere else. He ran out and pulled in a surprised looking Princess Twilight and Shining Armor into the room.

"What is this?" Shining Armor asked.

"This is my spaceship." The Doctor said happily.

"It is so… futuristic looking." Princess Twilight said.

"Wait until you see the outside of the ship." The Doctor said in total glee.

The Doctor and Romana chuckled at this little inside joke. The Doctor pressed the dematerialization lever and that iconic sound rang through the TARDIS.

"Where are we going?" Shining Armor asked.

"If I get it right, then we are going to the Moon!" The Doctor told them happily.

"The Moon?" Princess Twilight asked in disbelief.

"Yep. The Moon." Romana confirmed.

"What about Cadence, Princess Celestia, and your friend?" Shining Armor asked.

"Well, Princess Cadence is…" he paused, remembering that Shining Armor was married to Cadence. "I'll let you handle that one, Romana. And Princess Celestia and Daring Do are… already there, it seems. Well, let's go."

"Do you even know what's going to happen next?" Princess Twilight asked irritably.

"No. And that's the fun part." The Doctor said as he dematerialized the TARDIS. The call of the TARDIS rang out as they began their trip to the Moon where they would, at least potentially, save the world.


	6. Chapter 5: The Moonbase

Chapter 5: The Moonbase

**=The Moon of the Planet Gaia, 238, 857 Miles Above in Orbit, Canterlot Royal Palace, Palace Decorated Window Room, 1066 C.E. =**

The Doctor looked over the TARDIS console as the TARDIS came to land. "Well that's… odd." He declared.

"What's odd?" Princess Twilight asked.

"Now that we're all here on the Moon, all the life signs I was scanning for have apparently just vanished. Meaning that they all just decided to die for no reason, or they don't want it to be very easy to find them." The Doctor explained.

"Back up to that first part." Princess Twilight said. "Now that we're all here on the Moon? We could not be on the Moon. Everything in the ship stayed in one place, and I didn't feel us moving. I didn't feel the effects of a unicorn teleportation spell, and it would be difficult even for me to teleport this entire ship all the way to the Moon. So thusly, there is no way we could have moved from the spot we were before."

Shining Armor rolled her eyes. His sister was still the same way she was 63 years ago.

"I look forward to seeing her reaction when she steps out those doors." The Doctor muttered to Romana. Then he smiled and pressed the lever to open the TARDIS doors.

Princess Twilight strolled out, and was shocked to see they were in the middle of the Canterlot Royal Palace Throne Room. "What?" she asked herself. She ran over to the shattered windows, not even caring what they used to be, and looked out of it. She was even more shocked to see the surface of the Moon (which was no longer darkened.) and her home planet circling it in the distance. "WHAT?" she turned back to the Doctor to ask him a few questions, but was even more shocked to see a little blue box in place of the gigantic spaceship she had just been inside. "**WHAT?**" she screamed as she ran over to the box and stuck her head inside of it, once again seeing the gigantic spaceship inside of it. Her hooves began to buckle, and she collapsed to the floor, babbling incoherently.

"You know, I just might just start saying that in a future regeneration." The Doctor said in reference to the three whats that Twilight had said. Then he began to examine his surroundings.

Shining Armor was also surprised by the bigger on the inside thing, but his non scientific brain didn't try to understand it, so he just didn't know what to think of it.

The Doctor noted that all lights in the place had been shut off, but now that the surface of the Moon was no longer darkened, everything was now very dim. "That's spooky. There are two groups of ponies we need to find, and there are four of us. So, in the immortal words of juvenile Earth entertainment… 'Let's split up and look for clues!'"

Romana buried her face in her hooves while Shining Armor and Princess Twilight (who had gotten up off the floor) just looked confused.

"I'll go with Twilight, who, despite the fact that she believes in magic and won't believe in technology, seems to be the sort of smart one." The Doctor said.

"Hey!" Princess Twilight said in annoyance.

"And I suppose that leaves you with Shining Armor, who seems willing enough to help out." The Doctor said as he gestured to the two.

"I sort of take offense to that." Shining Armor sad through gritted teeth.

"I'll go towards Luna's room, even though we're not likely to find anypony there. I'll leave it up to you to see where you're going." He grabbed Twilight and walked off.

When they got to Luna's room, they could not entirely tell if anypony was there, as the room was even darker than the rest of the room. The Doctor examined the place, deciding to make casual conversation.

"So, how's it like ruling the kingdom? You seem a little young, so it would be stressful, am I correct?" The Doctor asked.

"I am actually 83 years old." Princess Twilight told him.

"You certainly don't look it." The Doctor said.

"It's a long story. You see, 66 years ago, Princess Celestia sent me to Ponyville to study the magic of friendship…"

"Metaphorically?" The Doctor interrupted.

Princess Twilight glared at him, and continued the story. "I made 5 good friends, and we lived a rather normal life for what was close to 3 years. Then I completed this magic spell, achieved my destiny, and became an immortal alicorn princess. That's the short version, anyway."

The Doctor looked at her with a completely blank expression. She thought for a second that he would burst out laughing again, but he didn't. "I sort of understand one of those parts, anyway." He noted.

"How so?" she asked in disbelief.

"At this moment, I'm 760 years old, and I'm still far away from dying." The Doctor noted.

"How can you be 760? Ordinary ponies don't live that long."

"But Time Lords do. Tell me, where are your friends now? How did you deal with the fact that every friend you have ever made eventually had to pass by?" he said in a slightly saddened voice, as if he was referring to himself just as much as he was she.

"They're all still alive at the moment. Happy, doing quite fine. Rainbow Dash hit her head a bit too hard during one of her daredevil moves and has memory issues now, but the rest are doing fine. But how are you doing?" Twilight said.

"Good, good." The Doctor said. "I wonder if we'll find anything here.

Suddenly, glowing catlike eyes darted by them.

"And there it is!" The Doctor said as he began following them.

**=The Moon of the Planet Gaia, 238, 857 Miles Above in Orbit, Canterlot Royal Palace, The Basement, 1066 C.E. =**

Romana and Shining Armor, however, had gotten off to a much more awkward start and middle with their search.

"What's down here that you think may be what we're looking for?" Romana asked.

"Not sure. But the Doctor is looking closer to the top of the castle, and we're looking at the bottom. Strategically, we'll cover more ground that way." He said.

"Do you have any military experience?" Romana asked.

"I used to be the Captain of the Royal Guard before I became the prince of the Crystal Empire and accepted immortality." Shining Armor said.

Romana nodded as she walked through the castle. "You wouldn't expect most castles to have a basement.

"They used to be part of crystal catacombs, but a part of them were closed off a few decades ago to be used for certain things like storage and retreat. I guess since it was connected to the castle, it was teleported up here with the rest of the castle to the Moon." Shining Armor explained.

"Interesting." Romana said.

All of a sudden, the chamber went completely dark. It was impossible to see anything. Then the lights came back on, and Romana was all alone.

Before she really had time to react, Daring Do came up behind her and grabbed her by the neck. "I have been examining you." She told her. "You are the youngest and most sustainable of the Time Lords, I believe you called yourself. You unique physiology is perfect for my cause. I thought I needed Luna's mind, but you will be even better for my plans. You will be mine."


	7. Chapter 6: A Change of Identity

Chapter 6: A Change of Identity

**=The Moon of the Planet Gaia, 238, 857 Miles Above in Orbit, Canterlot Royal Palace, Princess Luna's Room, 1066 C.E. =**

The Doctor followed the path of the catlike eyes quite closely. He looked behind himself to see that Princess Twilight was still closely following. He ran out of the room and began running down a long spiral staircase, quickly making his way towards the bottom. He made it to the bottom and ran through what looked like a hall for guests. He was very close to reaching the eyes, when suddenly…

The eyes they were following shimmered and disappeared. "An illusion." The Doctor realized. "To lead us away from what we were looking for, of to lead us into a trap? I wonder…"

"So what now?" Twilight asked him.

"I don't know, I don't know." The Doctor said.

Suddenly, two shadows ran next to them and darted out of the room.

"But I have feeling our opponent will stop at nothing to draw us out of this room. And while I am sure that something bad is going to happen to us if we leave the room, I think the others will be in a bit of trouble if we don't. Which, of course, leaves us with a bit of a dilemma." The Doctor finished.

**=The Moon of the Planet Gaia, 238, 857 Miles Above in Orbit, Canterlot Royal Palace, The Crystal Caverns Basement Section, 1066 C.E. =**

Romana felt something move through her body. She used all her willpower to push it back into the possessed Daring Do, but then she realized she didn't need all of it.

"No! You were not affected by the field from the eclipse!" Daring Do realized in anger."

Romana pushed her off in her distraction. Daring Do hit a wall and got stunned. "Sorry." She told her. She began running out of the basement, trying to both escape and find Shining Armor in the process. After searching around for a few moments, she gave up and ran up the stairs to get out of the room.

She got out of the room and began running through the large castle, trying to find somepony anywhere. She wished she had a map of the castle to figure out potential places where they would be hidden away. This castle was gigantic. She didn't know where anypony would be in here. She ran through a door into another room. She looked around and found nothing that she could use or nopony she was looking for. Wait a minute. She darted back into the room. She saw it was a mailroom for Princess Luna. There had to be something here she could use! She looked around and went to the most recent letters slot she opened it and opened the most recent letter. She saw from the envelope the letter was written by Princess Luna to Princess Luna!

"It certainly worked on her for awhile." She said to herself as she pulled out the letter and read it. The letter said that Nightmare Moon cold never leave her and there was no point in trying to run, hide away, as she was right there in her mind and it would be coming to take first her body and then her mind.

"But then it found me." Romana noted as she continued reading. The letter went on to say that every time this letter was opened, Nightmare Moon would talk to her in her mind, and soon it would break her by using all her friends and extended family to break through her.

"This might help me out a little. If it talks to her when the letter is opened, I can use a little bit of intelligence and Time Lady mentality to trace it back where it originated and find Luna! Should be easy enough." Romana said as she rolled up the letter and looked through it like a telescope. "Maybe I've been with the Doctor for a little too long." Romana said to herself as she frowned and walked out of the room.

She walked through the rooms for a moment before she found the room she was looking for. She entered another room and found Princess Luna hunched over in an ordinary closet, which was the last place anypony would think to look. She grabbed her and tried to drag her away, but found it practically impossible since Luna was nearly one and a half times her size.

She groaned and realized that this was going to be harder than she had originally thought. She made the hasty decision to just keep going, not caring that it was difficult. After all, there was no telling what would happen if 'Nightmare Moon's' plan succeeded.

After a while she made it into the entrance hall of the room, finding The Doctor and Twilight sitting on the steps of the room. She began carrying Luna over to them.

"Romana!" The Doctor exclaimed, happy to see her.

"Princess Luna! Is she alright?" Princess Twilight asked, very worried.

"Yes she's fine." Romana said as she set her down.

The Doctor and Twilight ran down to her. "You've been a big help to the cause, Romana. Now I can stop Nightmare Moon." He said gratefully. He then pulled out a pocket watch.

"You are going to hypnotize Princess Luna? That is the best plan you could come up with?" Princess Twilight asked in annoyance.

"Absolutely." The Doctor said as he began moving the watch in front of Luna's eyes.

"What, you are not going to say 'You are getting very sleepy?'" Princess Twilight whispered.

"No, I don't need to. And no distractions." The Doctor whispered back. He waved the watch for a few more seconds, and then stopped. "I just entered her mind and found out a few important pieces of information."

"Did you find out where Princess Celestia and my brother are?" Twilight asked hopefully.

"Actually, they've been atomized. Their entire life force has been strung into the fabric of the entire castle. Our opponent would expect us to look everywhere to find them, but they wouldn't expect us to look everywhere to find them." He said that last part as he motioned his hooves around the entire room.

Twilight gasped.

"That's what those illusions were. They were trying to draw us somewhere where we could help them. But never mind, we can help them now. I also found out that we can't destroy the last traces of Nightmare Moon from her mind from here through hypnosis, so I came up with an easier, yet much crazier plan." The Doctor explained.

"What's the plan?" Princess Twilight asked.

"This." The Doctor began to wave the watch once again. Luna's horn glowed, and everything around them flashed brightly.

Twilight looked out the window and was surprised to see the darkened streets of Canterlot once again. Princess Celestia and Shining Armor appeared in the middle of the room.

"The thing is, if my plan doesn't work, we're all doomed." The Doctor said.


	8. Chapter 7: Desperate Measures

Chapter 7: Desperate Measures

**=Gaia, Equestria, Canterlot, Canterlot Royal Palace, Great Hall, 1066 C.E. =**

In a dark colored flash of light, the possessed Daring Do appeared in the middle of the room, looking quite angry. "I will take you all." She said bitterly. "If you will not allow this, you will be destroyed."

"Then I suppose we'll all be destroyed, then." The Doctor said defiantly as he rushed down the stairs and through the long room to the door, motioning for the rest of the ponies in the room to the same. They all hurried as fast as they could to make to the door, after which the Doctor closed them down.

"That's not even going to slow her down, is it?" Romana said.

"No. But we need both the host of Nightmare Moon and Princess Luna present and watching to destroy the last traces of the Nightmare Moon personality from Luna's mind, thus releasing everything and setting it back in place. Of course, once this works, I'm going to have to latch the TARDIS into the planet and turn it back a little so the rotational cycle of the planet won't be thrown off."

With that, Daring Do teleported to the other side of the door and reappeared next to them.

"Now we just have to keep her occupied for 3 more minutes." The Doctor said.

"3 more minutes! You never mentioned that!" Romana snapped

"Look up there." The Doctor said.

Romana looked up to see that the Moon had set and was no longer visible. Her eyes widened in realization. "That is crazy…"

"Of course it is, I thought it up!" The Doctor said gleefully.

"It will definitely work, though." Romana noted.

They dodged Daring Do repeatedly as she tried to charge them and grab tem, still waiting for their plan to take shape.

"Annnnnnndddd…" The Doctor said as he watched the hilltop. "Now!"

Everypony looked up to see whatever it was he was talking about, but nopony except the Doctor and Romana could have ever prepared themselves for what it was. Princess Celestia, Princess Twilight, Shining Armor, Princess Luna, Nightmare Moon, none of them. Their eyes all widened in shock.

Without any magical intervention of any sort, or help, the Sun began to rise over the hilltops by itself.

The Doctor threw up his hooves to bask in both the sunlight and the fact that his plan had already worked.

Princess Luna looked shocked beyond anything. Her body seemed to fizz as she completely passed out to the ground.

Meanwhile the other personality, still using the body of Daring Do, hissed as she lost her grasp on the body as she turned into nothing but smoke, which went into the air as it dissolved into nothingness, leaving Daring Do stumbling about as her eyes returned to normal.

Princess Celestia and Twilight seemed more shocked than anypony. They could only watch in total shock before they fainted themselves out of the shock.

Shining Armor seemed just as shocked and confused, but he didn't faint.

The Doctor walked over to Daring Do. "Do I need to catch you up?" he asked.

"Actually, I remember everything that happened when I was possessed." Daring Do said as she brushed herself off. "Sorry about that."

"So it's over then?" Romana asked him.

"Not quite yet." The Doctor said, and with that, they all walked away to the TARDIS. Shining Armor saw them and followed them.

After a short walk, they all walked into the TARDIS, followed closely by Shining Armor.

The Doctor flipped a series of switches, followed by a loud crunch. "We're now connected to the center of the planet." The Doctor explained as he pressed a dematerialization switch. The TARDIS dematerialized, taking the whole planet with it. As the TARDIS rematerialized, The Doctor pressed a small switch. "I just took the whole planet to about a few hours before sunrise." The Doctor explained. "Then I sent out a recently installed hypnotizing pulse that made Everypony on the planet go their beds and go to sleep. They'll wake up and think it was a dream."

"What about Princess Celestia, Princess Luna, and Twiley?" Shining Armor asked, making his presence fully acknowledged.

"Right now they're in the process of willfully repressing the memory of the whole day, because it was simply too much for them. Any more questions?" he asked.

Shining Armor shook his head no, and then reached forward to shake his hoof. "I won't tell anypony. Thanks for saving the day, quite literally."

The Doctor shook his hoof. "You're welcome." The Doctor said.

Shining Armor smiled and walked out of the TARDIS.

"Well, I didn't change the course of the entire civilization, but I changed the life of one pony. I suppose that will have to do." The Doctor said a few moments later.

Romana and Daring Do smiled.

"For now."

Daring Do just groaned.

The Doctor just smirked as he looked down at the console and dematerialized the TARDIS.

**=The Time Vortex, The TARDIS, TARDIS Library, All of Time and Space =**

The Doctor walked out of the doors to the TARDIS library and walked through the corridors. He had just finished reading all of Equestria's history, and it was boring.

Everything was almost always peaceful and serene. He liked peace, but he **hated** complete serenity. He rounded the corner and walked into a darkened room. He clicked a button on what looked like an old time printer.

The purpose of the device was to search through time and space and find something worth investigating, and this would be their next destination.

A newspaper page printed out of it, and the Doctor picked it up and examined its contents. A wide smile crossed his face.

To be continued in Episode 5.

_Author's note: The main problem I ever had with other Doctor Who/ My Little Pony crossovers was that the Doctor immediately accepted that the ponies can do magic. The Doctor has __**never**__ believed in magic. That's one of the reasons I chose the 4__th__ Doctor. He has always been the least accepting of magic. So thus, humor is created. See you in Episode 5!_


End file.
